Periodic Boundary Conditions (PBC)

Tutorial 1 - Build a Trans-Polyacetylene Polymer From Ethylene, PBC/1D

1-1 Create a new molecule and corresponding view window by clicking on the "New" toolbar button.

1-2 Make the vinyl fragment (ethylene) the "Current Fragment" by double-clicking on the "R-Group Fragment" toolbar button and then clicking on the "vinyl" button in the "Select R-Group Fragment" dialog.

1-3 Click anywhere in the empty view window to create an ethylene molecule.

1-4 Center the molecule in the view window by clicking on the "Center" toolbar button.

1-5 Turn on atom labels for the view window by checking "Labels" from the "View" menu of the main window.

1-6 In the view window, click on atom 5 of ethylene to create a trans-butadiene molecule.

1-7 Show the PBC dialog for the molecule by selecting "PBC" from the "Edit" menu of the main window.

1-8 In the "Symmetry" tab of the PBC dialog, select "One" from the "Lattice Dimensions" combobox.

1-9 In the "Cell" tab of the PBC dialog, push down the "Place" button and make sure "Vertex" is selected to enable placement of the cell origin ("O (0)") vertex at any atom selected in the view window using the mouse. In the view window, click on atom 2.

1-10 In the "Cell" tab of the PBC dialog, select "a (1)" instead of "O (0)" to enable placement of the "a" cell vertex at any atom selected in the view window using the mouse. In the view window, click on atom 7.

1-11 In the "Cell" tab of the PBC dialog, select the "Delete All Atoms Outside Cell" item from the "Trim Contents" popup menu.

1-12 In the "Cell" tab of the PBC dialog, click on the "Center Contents" button.

1-13 At this point we have defined a primitive unit cell for a PBC/1D model of trans-polyacetylene polymer.

1-14 In the "View" tab of the PBC dialog, show two cells along the "a" axis using the corresponding spin box in the "Cell Replication" section. By default, the contents of replicate cells are shown in "Low Layer" format.

1-15 In the "View" tab of the PBC dialog, select "Normal" from the "Replicate Contents Format" combobox to show the contents of the replicate cells in the same format as the reference unit cell contents.

1-16 In the "Contents" tab of the PBC dialog, select the "Rebond Intercell" item from "Bonds" popup menu to update the bonding between atoms in adjacent cells.

1-17 Both of the unique CC bond lengths are too long in comparison to experiment. Change the intracell bond length between atoms 1 and 3 by clicking on the "Modify Bond" toolbar button and then clicking on atoms 1 and 3 in the same cell in the view window. In the corresponding "Semichem Smartslide" dialog, change the bond length value from 1.54 to 1.44 in the input field and then click on the OK button.

1-18 Change the intercell bond length between atoms 1 and 3 by clicking on the "Modify Bond" toolbar button and then clicking on atoms 3 and 1 in adjacent cells in the view window. In the corresponding "Semichem Smartslide" dialog, change the bond length value from 1.38253 to 1.36 in the input field and then click on the OK button.

1-19 In the In the "Contents" tab of the PBC dialog, select the "Rebond All" item from the "Bonds" popup menu to update the bonding between atoms in the same cell as well as in adjacent cells.

1-20 In the "View" tab of the PBC dialog, click on the "Combine" button in the "Cell Replication" section. This will cause the reference unit cell and the replicate unit cell shown on screen to be combined into a larger "supercell" which is twice the primitive unit cell. Note the atom number changes. Note also that the number of cells being viewed is automatically reduced to one.